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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: NAT10 (NCBI Gene ID:55226)


Gene Summary

check button Gene Summary
Gene InformationGene Name: NAT10
Gene ID: 55226
Gene Symbol

NAT10

Gene ID

55226

Gene NameN-acetyltransferase 10
SynonymsALP|Kre33|NET43
Cytomap

11p13

Type of Geneprotein-coding
DescriptionRNA cytidine acetyltransferase18S rRNA cytosine acetyltransferaseN-acetyltransferase 10 (GCN5-related)N-acetyltransferase-like protein
Modification date20200313
UniProtAcc

Q9H0A0


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0045727Positive regulation of translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneNAT10

GO:0045727

positive regulation of translation

30449621



check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
NAT10>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'NAT10[title] AND translation [title] AND human.'
GeneTitlePMID
NAT10..


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Exon Skipping Events

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.
all structure

check button Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF
ENST000002578293413972634139841Frame-shift
ENST000002578293416073734160834Frame-shift
ENST000002578293416093134161042In-frame
ENST000002578293416263534162755In-frame
ENST000002578293416326534163364In-frame
ENST000002578293416499134165075In-frame

check button Exon skipping position in the amino acid sequence.
ENSTExon skip start (DNA)Exon Skip end (DNA)Len(transcript seq)Exon skip start (mRNA)Exon Skip end (mRNA)Len(amino acid seq)Exon skip start (AA)Exon Skip end (AA)
ENST0000025782934160931341610424019251526251025769806
ENST0000025782934162635341627554019279929181025864904
ENST0000025782934163265341633644019291930171025904937
ENST0000025782934164991341650754019309231751025962989

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.
Q9H0A090493711025ChainID=PRO_0000215883;Note=RNA cytidine acetyltransferase
Q9H0A086490411025ChainID=PRO_0000215883;Note=RNA cytidine acetyltransferase
Q9H0A076980611025ChainID=PRO_0000215883;Note=RNA cytidine acetyltransferase
Q9H0A096298911025ChainID=PRO_0000215883;Note=RNA cytidine acetyltransferase
Q9H0A09049377021025RegionNote=Required for localization to the nucleolus and midbody;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19303003;Dbxref=PMID:19303003
Q9H0A08649047021025RegionNote=Required for localization to the nucleolus and midbody;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19303003;Dbxref=PMID:19303003
Q9H0A07698067021025RegionNote=Required for localization to the nucleolus and midbody;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19303003;Dbxref=PMID:19303003
Q9H0A09629897021025RegionNote=Required for localization to the nucleolus and midbody;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19303003;Dbxref=PMID:19303003
Q9H0A0904937934934Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q9H0A0962989984984Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q9H0A0962989987987Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163
Q9H0A0962989983983Natural variantID=VAR_061894;Note=A->T;Dbxref=dbSNP:rs36006049
Q9H0A0864904879879Sequence conflictNote=Q->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9H0A0962989971971Sequence conflictNote=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305


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Expression


check buttonGene expression level across TCGA pancancer
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check buttonGene expression level across GTEx pantissue
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check buttonExpression level of gene isoforms across TCGA pancancer
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check buttonExpression level of gene isoforms across GTEx pantissue
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check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
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check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval
CHOLNAT10-3.098174907947420.00390625
PRADNAT10-1.170807232862440.00496210155254694
KICHNAT10-2.202063620778181.50799751281738e-05
STADNAT10-6.132889981235721.72760337591171e-07
KIRCNAT10-1.406245700116911.96258882516009e-11
KIRPNAT10-1.083944465647032.3283064365387e-09
LUADNAT10-3.074137699906183.40660700589176e-10


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
OVNAT10hsa-miR-28-5p630.3524289251259280.0107546364056926
UCECNAT10hsa-miR-28-5p63-0.4411000763941940.00959161249815749


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
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Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through copy number variation of Translation factor
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Cancer typeGeneCoefficientPvalue

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with NAT10 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)
all structure
Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue
COADCell metabolism geneNAT10POLR1B0.8031433391.56E-75
COADEpifactorNAT10KAT2A0.8067805741.02E-76
COADIUPHARNAT10KAT2A0.8067805741.02E-76


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure

check buttonOverlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure
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* Edge colors based on TCGA cancer types.

check button* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
LUSCNAT10RRP9-1.883240974019740.00013362071971533
LIHCNAT10UTP18-1.48140876285780.000201991820198738
KICHNAT10UTP181.665772448507770.000329077243804932
HNSCNAT10NOL101.919625888748330.000507211686226584
KIRPNAT10UTP18-1.30471450640120.000837184488773346
LUADNAT10RRP9-1.264490274448590.00127825845990135
LIHCNAT10NOP58-4.336985364774340.00149357664052089
ESCANAT10UTP18-1.762361971219720.001953125
ESCANAT10BYSL-1.419654323280340.0029296875
CHOLNAT10RRP9-2.075017026213320.00390625
CHOLNAT10UTP18-2.581753666786330.00390625
PRADNAT10UTP6-1.378045849303610.00468840651979362
ESCANAT10RRP9-1.052603290677210.013671875
ESCANAT10AATF-1.659369155631480.0185546875
UCECNAT10BMS12.172685266319410.03125
ESCANAT10UTP202.152665862094620.0419921875
STADNAT10UTP6-1.774107921781941.10594555735588e-06
KIRPNAT10BMS1-1.912472284250911.11940316855908e-05
KIRPNAT10AATF-2.841288566213191.26352533698082e-05
KIRPNAT10UTP6-1.813351161663151.2875534594059e-06
KIRCNAT10AATF-3.466416525911632.11933773649914e-11
STADNAT10BYSL-2.469966828668352.3283064365387e-09
BRCANAT10AATF-1.54066283708872.62695618358088e-10
KIRPNAT10NOL6-1.665664650655183.51201742887497e-06
PRADNAT10NOL10-3.432045087059413.77428293642232e-05
BRCANAT10NOL6-2.542437945648413.94048164550614e-07
STADNAT10RRP9-3.903919728761914.09781932830811e-08
PRADNAT10BYSL-4.188341724498794.1396395841136e-09
LIHCNAT10AATF-5.41170776826364.22970612218234e-07
LIHCNAT10UTP6-2.53262499409144.2584580238307e-05
HNSCNAT10BYSL1.830071342279695.27545735167224e-05
PRADNAT10NOP58-1.453777413716325.36984323097516e-05
STADNAT10UTP18-1.225547798197835.8719888329506e-07
KIRPNAT10RRP9-1.717052153072075.97489997744561e-06
KIRCNAT10UTP6-1.44062060701646.13427141633893e-11
LUADNAT10AATF-5.449788652325757.09793428673073e-08
THCANAT10UTP61.372913961213817.52915292268072e-05
BRCANAT10BYSL-3.724402728413627.85448425978448e-18
KICHNAT10UTP61.581593987325878.34465026855468e-07


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with NAT10
LYAR, OTUB1, tat, TERT, TOP1, SIRT1, SIRT7, CUL3, CUL1, CAND1, GRK5, UTP20, DGCR8, DHX37, ESR1, FN1, ITGA4, BRCA1, CUL7, OBSL1, UBE2I, SUZ12, EED, RNF2, BMI1, ABCE1, FBXW11, NOL12, RPS2, RPS8, THUMPD1, NTRK1, ABCF2, EIF4G1, DDX18, IMP4, NOP58, RPS5, SRPK1, SSB, NOP2, RPL5, TSR1, IFI16, gag, HNRNPU, NPM1, RPL10, VIM, TFG, SYNCRIP, NOP56, IBTK, Eif3a, Eif3e, Srp72, 2310003H01Rik, Rrbp1, Ncaph, MCM5, CDC5L, TP53, MDM2, UBE2D2, UBC, C1orf131, CDC14B, NOL10, HIST1H1T, RPS14, ZNF512, MECP2, RPL18A, ZNF169, GPATCH4, FGF8, RRP8, RPS11, LASP1, TRIM25, MTF1, HNRNPL, LEO1, NAT10, ZNF574, PCBP1, CHD3, CHD4, LARP7, CDC34, RIOK1, HERC2, DCPS, TNRC6A, RBBP5, MYC, AURKB, CANX, CDK7, FBL, HIST1H3A, RAB11A, RPS6, TGOLN2, AURKAIP1, GRWD1, KIAA1429, DCAF13, RC3H1, NR2C2, PPARG, RPS6KA2, XRCC6, PRDM16, MECOM, HIST1H4A, SCARB2, HMGB1, BIRC3, STAU1, NFX1, WWP2, BRD7, SOX2, PLEKHA4, MORC2, PARP1, FANCD2, CCDC84, ZC3H18, MAP2K1, MYLK2, NCL, M, nsp13, nsp14, nsp4, nsp6, ORF14, ORF3a, ORF7a, ORF7b, SMC3, PDS5A, UBR5, CIT, ANLN, CHMP4B, CHMP4C, ECT2, KIF14, KIF20A, KIF23, PRC1, BRD2, MNDA, CHCHD1, SUMO2, MAFB, NUPR1, BRD4, Apc2, vpr, DNAJC9, MKRN1, DDX58, DDRGK1, ISG15, APEX1, CD3EAP, DDX23, DHX40, HIST1H2BG, NIFK, POLR1E, RPL31, RPS24, CIRH1A, ZNF330, FZR1, WDR5, NAA40, ZBTB2, RPS3, PNMAL1, MAGEB2, CCDC140, HIST2H2AC, HIST1H1C, SRSF4, KAL1, GLI4, NPM3, RPL4, NEURL4, RBM28, CBX6, RPL17, RPL13A, NMNAT1, ABT1, C12orf43, RPL13, CCDC137, LIN28B, AATF, APOBEC3C, RPS10, FGF13, RPL26L1, RPL19, ZNF467, H1FNT, RPL23A, HIST1H2AM, SELM, SRSF6, NGDN, H2AFB2, RPL23AP32, RBM19, RPSA, SURF6, RBM4B, RPSAP58, SRSF1, LIN28A, SENP3, FGFBP1, NEIL1, RPS19, RPL3, USE1, RPL35, YES1, RPS3A, RPLP0, KRR1, HIST1H1E, ZNF668, HIST1H1A, EP300, FBXW7, SREK1, CD2BP2, nsp1, DPP4, HECTD1, N, SIRT6, KLF16, BRD3,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
NAT10chr1134130357TCsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variant,SO:0001627|intron_variantSO:0001819|synonymous_variant,SO:0001627|intron_variant
NAT10chr1134133671CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134133767GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134135256CTsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
NAT10chr1134135349CTsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134139778GAsingle_nucleotide_variantBenignnot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134139840CTsingle_nucleotide_variantBenignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
NAT10chr1134152464CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
NAT10chr1134154641CTsingle_nucleotide_variantBenignnot_specifiedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134161951GCsingle_nucleotide_variantUncertain_significancenot_providedSO:0001819|synonymous_variantSO:0001819|synonymous_variant
NAT10chr1134163339CTsingle_nucleotide_variantLikely_benignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant
NAT10chr1134163901GCsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
NAT10chr1134165053GAsingle_nucleotide_variantBenignnot_providedSO:0001583|missense_variantSO:0001583|missense_variant


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples

check buttonCopy number variation (CNV) of NAT10
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across NAT10
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


check button Fusion genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
23307SARCTCGA-DX-A6YS-01AADAM19chr5156933782-NAT10chr1134165074-
23307SARCTCGA-DX-A6YS-01AADAM19chr5156934063-NAT10chr1134160115-
23307N/ABQ027507CSDE1chr1115259537-NAT10chr1134135187+
74063N/AAW023035NAT10chr1134168455+C9chr539319135-
71295BRCATCGA-AN-A0XU-01ANAT10chr1134130380+CAPRIN1chr1134118026+
71295OVTCGA-13-1501-01ANAT10chr1134127339+CAPRIN1chr1134118026+
82394SARCTCGA-SI-A71Q-01ANAT10chr1134145402+METTL15chr1128420335+
98420OVTCGA-24-1425NAT10chr1134133770+SLC3A2chr1162655606+


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
all structure
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
THCANAT100.005139648211130720.14
TGCTNAT100.007644905149716970.21
PAADNAT100.01132296394195550.29
KIRPNAT100.01421445435893480.36
ESCANAT100.02477947723226160.59
CHOLNAT100.0488354577408591

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
Cancer typeTranslation factorpvaladj.p
LGGNAT100.001565354010119430.05
PRADNAT100.03695070214530721
PAADNAT100.02466329989950160.74
OVNAT100.001626047601330960.05
ESCANAT100.0002028240806334810.0067

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source